diff --git a/src/CountMinSketch.hpp b/src/CountMinSketch.hpp index bd3edc9231b956156e5472ade065d692f040d530..b552a286802d4d38fe297a773ab1da4b53f86550 100644 --- a/src/CountMinSketch.hpp +++ b/src/CountMinSketch.hpp @@ -24,7 +24,7 @@ typedef struct { int lambda; int kappa; int kappa_prime; - int filter_size; // max amount of RAM wanted for the CMS. + int max_filter_size; // max amount of RAM wanted for the CMS. int filter_PE_separately; // indicates whether PE reads must be treated as single by the cms. Indeed it may appear that 1 end contains useful k-mer but that other end contains k-mer such that "global" median is below threshold. // In this case, read is rejected by the CMS (default behavior). We want to do an experimentation to see if keeping such reads wold lead to better results in assembling. // Values can be 0 (process PE as single),1 (process PE separately with strict implementation for kappa_prime) or 2 (process PE separately with lenient implementation for kappa prime). diff --git a/src/ROCKparams.h b/src/ROCKparams.h index 56f63882ab7f27553ec52a9a1d590847ecc648c0..5a5e1b43f7358ee65b538fb922608ce67096e577 100755 --- a/src/ROCKparams.h +++ b/src/ROCKparams.h @@ -60,6 +60,7 @@ class ROCKparams{ vector<PE_files> v_PE_files; int f_id; unsigned long cms_size; + //unsigned long total_machine_RAM; float expected_collision_proba; @@ -109,14 +110,17 @@ public: cms_size=0; expected_collision_proba=0.0; //! collision probability that is computed at the beginning of ROCK from the expected number of distinct k-mers provided by the user. //min_correct_k_mers_in_read=0; - parms.filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory - if (parms.filter_size==0) throw EXIT_FAILURE; + //total_machine_RAM=getNodePhysMemory(); + parms.max_filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory + if (parms.max_filter_size==0) throw EXIT_FAILURE; } void initFromMainOptsArgs(int argc,char ** argv); + + CMSparams getCMSparams() const { return parms; }